You should not have to select the designer files. Once you select the form file, VS should automatically grab the designer file. That is why you can only select one at a time, otherwise it will not grab the designer file. If you have resources, you will need to also add that back to the project.
Since you are using c#, this may be an easier way:
1) Download and extract version 3.99x
2) Replace the AdvancedHMIcs folder with the same folder from your previous project
3) Open 3.99x in Visual Studio
4) Build the solution
This is similar to what you did previously, except you do not have to delete the project and add existing within VS.
After you build the project, use Windows Explorer to check the properties of the DLL files that are with the executable to see if they are version 3.9.24